DNA methylation is an important epigenetic modification. However, the regulations and functions of insect intragenic DNA methylation remain unknown. Here, we demonstrate that a regulatory mechanism involving intragenic DNA methylation controls ovarian and embryonic developmental processes in Bombyx mori. In B. mori, DNA methylation is found near the transcription start site (TSS) of ovarian genes. By promoter activity analysis, we observed that 5′ UTR methylation enhances gene expression. Moreover, methyl-DNA-binding domain protein 2/3 (MBD2/3) binds to the intragenic methyl-CpG fragment and recruits acetyltransferase Tip60 to promote histone H3K27 acetylation and gene expression. Additionally, genome-wide analyses showed that the peak of H3K27 acetylation appears near the TSS of methyl-modified genes, and DNA methylation is enriched in genes involved in protein synthesis in the B. mori ovary, with MBD2/3 knockdown resulting in decreased fecundity. These data uncover a mechanism of gene body methylation for regulating insect gene expression and reproduction.

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Published in iScience, v. 24, issue 2, 102040.

© 2021 The Author(s)

This is an open access article under the CC BY-NC-ND license (https://creativecommons.org/licenses/by-nc-nd/4.0/).

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This work was supported by the National Natural Science Foundation of China (No. 31872286).

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The raw Illumina sequencing data from the BS-seq and RNA-seq generated during this study are deposited in SRA under accession number SRP217273 at NCBI.

1-s2.0-S2589004221000080-mmc1.pdf (1235 kB)
Document S1. Transparent methods, Figures S1–S9, and Tables S1, S5–S8, and S10.

1-s2.0-S2589004221000080-mmc2.xls (13565 kB)
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Table S3. DNA methylation levels of all genes in the genome of silkworm ovaries by BS-seq analysis, related to Figures 1 and 2.

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Graphical abstract